Jose Tomas Atria (JIRA | 1 Feb 02:04 2015
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[jira] [Created] (UIMA-4212) Add methods to CasUtil to select and index intersecting annotations

Jose Tomas Atria created UIMA-4212:
--------------------------------------

             Summary: Add methods to CasUtil to select and index intersecting annotations
                 Key: UIMA-4212
                 URL: https://issues.apache.org/jira/browse/UIMA-4212
             Project: UIMA
          Issue Type: Improvement
          Components: uimaFIT
            Reporter: Jose Tomas Atria
            Priority: Minor
         Attachments: selectIntersects.patch

CasUtil includes methods to select and index covered and covering annotations of a given type (ie,
supersets and subsets of an annotation's interval).

The attached patch adds methods to select and index intersecting annotations,  either including covering
annotations or not.

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Jose Tomas Atria (JIRA | 1 Feb 02:04 2015
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[jira] [Updated] (UIMA-4212) Add methods to CasUtil to select and index intersecting annotations


     [
https://issues.apache.org/jira/browse/UIMA-4212?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Jose Tomas Atria updated UIMA-4212:
-----------------------------------
    Attachment: selectIntersects.patch

> Add methods to CasUtil to select and index intersecting annotations
> -------------------------------------------------------------------
>
>                 Key: UIMA-4212
>                 URL: https://issues.apache.org/jira/browse/UIMA-4212
>             Project: UIMA
>          Issue Type: Improvement
>          Components: uimaFIT
>            Reporter: Jose Tomas Atria
>            Priority: Minor
>              Labels: newbie, patch
>         Attachments: selectIntersects.patch
>
>
> CasUtil includes methods to select and index covered and covering annotations of a given type (ie,
supersets and subsets of an annotation's interval).
> The attached patch adds methods to select and index intersecting annotations,  either including
covering annotations or not.

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(Continue reading)

Frank Xu (JIRA | 30 Jan 20:00 2015
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[jira] [Updated] (UIMA-4210) Client hangs with more than 1 time-out


     [
https://issues.apache.org/jira/browse/UIMA-4210?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Frank Xu updated UIMA-4210:
---------------------------
    Description: 
The client hangs if the execution has two time-outs. After debugging into the issue, we figure out that the
resending mechanism has some bugs in it. Here are the detailed description.

Please review the necessity for the invocation of sendCas(). In our system, we don't have to resend the CAS
to process again. Please provide a configuration so that we don't have to resend the CAS every time there is
a time out.

Whenever there is the first time-out, BaseUIMAAsynchronousEngine_impl#notifyOnTimout() is invoked
and it hangs when it tries to invoke sendCas() at line 2385. I believe the reason is that the sendCas() is a
synchronized method and a potential threading issue causes this thread hang over there. Please be noted
that this block is also synchronized.

Then when there is a second time-out, it will be hanging in the very beginning of the method
notifyOnTimeout() and cannot clear the time-out CAS from the CAS list, which hangs the entire client.

  was:
The client hangs if the execution has two time-outs. After debugging into the issue, we figure out that the
resending mechanism has some bugs in it. Here are the detailed description.

Please review the necessity for the invocation of sendCas(). In our system, we don't have to resend the cas
to process again. Please provide a configuration so that we don't have to resend the case every time there
is a time out.

(Continue reading)

Lou DeGenaro (JIRA | 30 Jan 21:16 2015
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[jira] [Created] (UIMA-4211) DUCC Web Server (WS) enable request logging

Lou DeGenaro created UIMA-4211:
----------------------------------

             Summary: DUCC Web Server (WS) enable request logging
                 Key: UIMA-4211
                 URL: https://issues.apache.org/jira/browse/UIMA-4211
             Project: UIMA
          Issue Type: Improvement
          Components: DUCC
            Reporter: Lou DeGenaro
            Assignee: Lou DeGenaro
            Priority: Minor
             Fix For: 2.0.0-Ducc

Enable WS request logging.

In ducc.properties, use ducc.ws.requestLog.RetainDays = <value> to control number of days to retain. 
The value 0 disables recording altogether.
Changing the value requires WS restart to become effective.

Logs are written to DUCC_HOME/logs/webserver.

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Lou DeGenaro (JIRA | 30 Jan 21:35 2015
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[jira] [Resolved] (UIMA-4211) DUCC Web Server (WS) enable request logging


     [
https://issues.apache.org/jira/browse/UIMA-4211?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Lou DeGenaro resolved UIMA-4211.
--------------------------------
    Resolution: Fixed

Code is delivered.

> DUCC Web Server (WS) enable request logging
> -------------------------------------------
>
>                 Key: UIMA-4211
>                 URL: https://issues.apache.org/jira/browse/UIMA-4211
>             Project: UIMA
>          Issue Type: Improvement
>          Components: DUCC
>            Reporter: Lou DeGenaro
>            Assignee: Lou DeGenaro
>            Priority: Minor
>             Fix For: 2.0.0-Ducc
>
>
> Enable WS request logging.
> In ducc.properties, use ducc.ws.requestLog.RetainDays = <value> to control number of days to retain. 
The value 0 disables recording altogether.
> Changing the value requires WS restart to become effective.
> Logs are written to DUCC_HOME/logs/webserver.

(Continue reading)

Frank Xu (JIRA | 30 Jan 19:40 2015
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[jira] [Created] (UIMA-4210) Client hangs with more than 1 time-out

Frank Xu created UIMA-4210:
------------------------------

             Summary: Client hangs with more than 1 time-out
                 Key: UIMA-4210
                 URL: https://issues.apache.org/jira/browse/UIMA-4210
             Project: UIMA
          Issue Type: Bug
          Components: Eclipse plugins
    Affects Versions: 2.4.2AS
         Environment: Java 7, Mac OS
            Reporter: Frank Xu

The client hangs if the execution has two time-outs. After debugging into the issue, we figure out that the
resending mechanism has some bugs in it. Here are the detailed description.

Please review the necessity for the invocation of sendCas(). In our system, we don't have to resend the cas
to process again. Please provide a configuration so that we don't have to resend the case every time there
is a time out.

Whenever there is the first time-out, BaseUIMAAsynchronousEngine_impl#notifyOnTimout() is invoked
and it hangs when it tries to invoke sendCase() at line 2385. I believe the reason is that the sendCase() is a
synchronized method and a potential threading issue causes this thread hang over there. Please be noted
that this block is also synchronized.

Then when there is a second time-out, it will be hanging in the very beginning of the method
notifyOnTimeout() and cannot clear the time-out case from the cas list, which hangs the entire client.

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Frank Xu (JIRA | 30 Jan 20:13 2015
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[jira] [Updated] (UIMA-4210) Client hangs with more than 1 time-out


     [
https://issues.apache.org/jira/browse/UIMA-4210?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Frank Xu updated UIMA-4210:
---------------------------
    Description: 
The client hangs if the execution has two time-outs. After debugging into the issue, we figure out that the
resending mechanism has some bugs in it. Here are the detailed description.

Please review the necessity for the invocation of sendCAS(). In our system, we don't have to resend the CAS
to process again. Please provide a configuration so that we don't have to resend the CAS every time there is
a time out.

Whenever there is the first time-out, BaseUIMAAsynchronousEngine_impl#notifyOnTimout() is invoked
and it hangs when it tries to invoke sendCas() at line 2385. I believe the reason is that the sendCAS() is a
synchronized method and a potential threading issue causes this thread hang over there. Please be noted
that this block is also synchronized.

Then when there is a second time-out, it will be hanging in the very beginning of the method
notifyOnTimeout() and cannot clear the time-out CAS from the CAS list, which hangs the entire client.

  was:
The client hangs if the execution has two time-outs. After debugging into the issue, we figure out that the
resending mechanism has some bugs in it. Here are the detailed description.

Please review the necessity for the invocation of sendCas(). In our system, we don't have to resend the CAS
to process again. Please provide a configuration so that we don't have to resend the CAS every time there is
a time out.

(Continue reading)

Jim Challenger (JIRA | 30 Jan 16:09 2015
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[jira] [Created] (UIMA-4209) DUCC viz: use service id instead of service instance ID in display.

Jim Challenger created UIMA-4209:
------------------------------------

             Summary: DUCC viz: use service id instead of service instance ID in display.
                 Key: UIMA-4209
                 URL: https://issues.apache.org/jira/browse/UIMA-4209
             Project: UIMA
          Issue Type: Improvement
          Components: DUCC
    Affects Versions: 1.1.0-Ducc
            Reporter: Jim Challenger
            Assignee: Jim Challenger
             Fix For: 2.0.0-Ducc

Use the registered service id and conflate instances on the same node, analogous to the treatment for jobs,
in the visualization.

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Marshall Schor (JIRA | 29 Jan 21:52 2015
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[jira] [Resolved] (UIMA-4198) cleanup CasCopier - move test out of inner loop, improve tst


     [
https://issues.apache.org/jira/browse/UIMA-4198?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Marshall Schor resolved UIMA-4198.
----------------------------------
    Resolution: Fixed

> cleanup CasCopier - move test out of inner loop, improve tst
> ------------------------------------------------------------
>
>                 Key: UIMA-4198
>                 URL: https://issues.apache.org/jira/browse/UIMA-4198
>             Project: UIMA
>          Issue Type: Improvement
>            Reporter: Marshall Schor
>            Assignee: Marshall Schor
>            Priority: Minor
>             Fix For: 2.7.0SDK
>
>
> Make runtime range checking conditional on their being same features with different range types - this
will skip the range check in most cases.  Improve test case to have an instance of this

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Marshall Schor (JIRA | 29 Jan 21:51 2015
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[jira] [Resolved] (UIMA-4208) JSON: ordering of subtypes of Annotation base not correct


     [
https://issues.apache.org/jira/browse/UIMA-4208?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Marshall Schor resolved UIMA-4208.
----------------------------------
    Resolution: Fixed

> JSON: ordering of subtypes of Annotation base not correct
> ---------------------------------------------------------
>
>                 Key: UIMA-4208
>                 URL: https://issues.apache.org/jira/browse/UIMA-4208
>             Project: UIMA
>          Issue Type: Bug
>          Components: Core Java Framework
>            Reporter: Marshall Schor
>            Assignee: Marshall Schor
>             Fix For: 2.7.0SDK
>
>
> The sort comparator has a cut/paste typo - it doesn't compare the feature passed in.

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Apache Jenkins Server | 29 Jan 21:51 2015
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Build failed in Jenkins: UIMA-SDK #683

See <https://builds.apache.org/job/UIMA-SDK/683/>

------------------------------------------
Started by an SCM change
Building remotely on windows1 (Windows) in workspace <https://builds.apache.org/job/UIMA-SDK/ws/>
Cleaning local Directory trunk
java.io.IOException: remote file operation failed: <https://builds.apache.org/job/UIMA-SDK/ws/>
at hudson.remoting.Channel <at> 746335ce:windows1
	at hudson.FilePath.act(FilePath.java:916)
	at hudson.FilePath.act(FilePath.java:893)
	at hudson.scm.SubversionSCM.checkout(SubversionSCM.java:936)
	at hudson.scm.SubversionSCM.checkout(SubversionSCM.java:871)
	at hudson.model.AbstractProject.checkout(AbstractProject.java:1252)
	at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:615)
	at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:86)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:524)
	at hudson.model.Run.execute(Run.java:1706)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:529)
	at hudson.model.ResourceController.execute(ResourceController.java:88)
	at hudson.model.Executor.run(Executor.java:232)
Caused by: java.nio.file.AccessDeniedException: <https://builds.apache.org/job/UIMA-SDK/ws/trunk\.svn\all-wcprops>
	at sun.nio.fs.WindowsException.translateToIOException(Unknown Source)
	at sun.nio.fs.WindowsException.rethrowAsIOException(Unknown Source)
	at sun.nio.fs.WindowsException.rethrowAsIOException(Unknown Source)
	at sun.nio.fs.WindowsFileSystemProvider.implDelete(Unknown Source)
	at sun.nio.fs.AbstractFileSystemProvider.delete(Unknown Source)
	at java.nio.file.Files.delete(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor825.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.lang.reflect.Method.invoke(Unknown Source)
(Continue reading)


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